toGC: a new tool for correcting errors in gene annotations using RNA-seq data

The accuracy of genomic annotation is crucial for subsequent functional investigations; however, computational protocols used in high-throughput annotation of open reading frames (ORFs) can introduce inconsistencies. These inconsistencies, which lead to non-uniform extension or truncation of sequence ends, pose challenges for downstream analyses. Existing strategies to rectify these inconsistencies are time-consuming and labor-intensive, lacking specific approaches.

To address this gap, a team of researchers from China developed toGC, a tool that integrates genomic annotation with RNA-seq datasets to rectify annotation inconsistencies. They reported their results in the Journal of Integrative Agriculture.

“Using toGC, we achieved an accuracy of nearly 100% accuracy in correcting inconsistencies in published Phytophthora sojae ORFs,” shares corresponding author Yuanchao Wang, a professor at Nanjing Agricultural University. “We applied this innovative pipeline to the GPCR-bigrams gene family, which was predicted to have 42 members in the P. sojae genome but lacked experimental validation.”

By employing toGC, the researchers identified 32 GPCR-bigram ORFs with inconsistencies between previous annotations and toGC-corrected sequences. Notably, among these were 5 genes (GPCR-TKL9, GPCR-TKL15, GPCR-PDE3, GPCR-AC3, and GPCR-AC4) showed substantial inconsistencies.

“Experimental gene annotation confirmed the effectiveness of toGC, as sequences obtained through cloning matched those annotated by toGC,” adds Wang. “We discovered two novel GPCRs (GPCR-AC3 and GPCR-AC4), which were previously mispredicted as a single gene.” 

CRISPR/Cas9-mediated knockout experiments revealed the involvement of GPCR-AC4, but not GPCR-AC3 in oospore production, further confirming their status as two separate genes.

“In addition to P. sojae, the reliability of the toGC pipeline in Phytophthora capsici and Pythium ultimum 

further emphasizes the robustness of this pipeline,” shares co-corresponding author Ming Wang, a professor at Nanjing Agricultural University. “Our findings highlight the utility of toGC for reliable gene model correction, facilitating investigations into biological functions and offering potential applications in diverse species analyses.”

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Contact the author: Min Qiu, E-mail: minqiu@njau.edu.cn; Chun Yan, E-mail: 2022202060@stu.njau.edu.cn; #Correspondence Yuanchao Wang, E-mail: wangyc@njau.edu.cn; Ming Wang, E-mail: mwang@njau.edu.cn

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